You can check your PCIe energy policy on this file:
# cat /sys/module/pcie_aspm/parameters/policy
Since Gen3 are pretty straightforward on power management through ASPM(Active-State Power Management ), this could be the root cause of the issue on your bus: The throughput is low so, the modules reduces the speed but it forgets to increase it again when needed(if needed). You could enforce on grub to avoid using the "powersave" or the "default" policy by disabling aspm with the following parameter:
pcie_aspm=off
Test this on just one kernel appending this option at /boot/grub/grub.conf on the "kernel" line of your default boot linux. Example of grub config extracted from the Red Hat docs:
default=0
timeout=10
splashimage=(hd0,0)/grub/splash.xpm.gz
hiddenmenu
title Red Hat Enterprise Linux Server (2.6.18-2.el5PAE)
root (hd0,0)
kernel /boot/vmlinuz-2.6.18-2.el5PAE ro root=LABEL=/1 rhgb quiet pcie_aspm=off
initrd /boot/initrd-2.6.18-2.el5PAE.img